MolNFT v1 · #90613 · protein
Thr 160 phosphorylated CDK2 K89D, Q131E - human cyclin A3 complex with the inhibitor RO3306
4EOI · Cyclin-dependent kinase 2: “Thr 160 phosphorylated CDK2 K89D, Q131E - human cyclin A3 complex with the inhibitor RO3306”. X-ray diffraction, 1 ligand (1RO), 11 pockets (best druggability 0.81). MolNFT v1 #90613 on GenesisL1: 3D…
- PDB
- 4EOI
- Type
- protein
- Length
- 1,105 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- 1RO
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 295 | 36% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 67% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 297 | 34% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- 1RO · (5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one · ligand · 2 copies · chains A, C
- SGM · Monothioglycerol · additive · 2 copies · chains A, B, D
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.81 | 0.99 | 24 | empty |
| 2 | 114 | 0.80 | 0.99 | 22 | empty |
| 3 | 992 | 0.77 | 0.79 | 98 | empty |
| 4 | 213 | 0.72 | 0.88 | 30 | 1RO |
| 5 | 215 | 0.69 | 0.86 | 26 | 1RO |
Interfaces
5 interfaces between chains.
- C–D · 1638 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1623 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, additive adduct).
Compared structures
- 4EOI · Thr 160 phosphorylated CDK2 K89D, Q131E - human cyclin A3 complex with the inhibitor… · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P24941
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 4EOI · PDBe 4EOI · UniProt P24941 · UniProt P20248
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